Well, yes, I tried to figure out how to use it, but nothing worked. How can refactoring be automated anyway? I thought it was a manual rethinking and restructuring process.

Here I meant not refactoring as rethinking process but as set of tools which help to change code after rethinking.
In some cases automatic method extracting or smart renaming (in all files of project) help to save time for me.

How can refactoring be automated anyway? I thought it was a manual rethinking and restructuring process.

A lot of operations from Fowler's, Refactoring: Improving the Design of Existing Code, can be automated. Java under Eclipse has had these for a long time now. A huge time saver when attacking God objects and procedural code in classes, and extracting methods.

I use Eclipse ganymede at work for Java, I recently tried using it for PHP. I think I may give Netbeans a try for PHP dev..

Don't waste your time with Netbeans. Stick with Eclipse PDT.

Tried Netbeans for few weeks and found it very slow (kept refreshing the workspace all the time even though I didn't change anything), it has very poor debuging features (with XDEBUG at least) and a few annoying bugs (ALT+TAB on Windows is the most annoying bug! The menu kept activating and the supposed solution didn't work for me). This is just to list a few...

I'm using code lobster (http://www.codelobster.com/), 3.5
mainly because I liked the code-igniter plugin and got used to it
they are working on a Yii plugin as I asked them recently.

good thing it's free and you only pay extra for any specific framework
plugins, not too expensive about $25

Warning There are a few bugs but I think generally I have not had too many problems,
they do regular releases to iron problems and has got better over time,
quite handy just to use without any paid for plugins for free.

I tried and try many IDE but the end result does not have the complete discretion.
First. PHPDESIGNER (NiceCode incomplete, Cant custom new line on array yii systax)
Zend Studio (Not support auto complete variables from CController, php Core lackof function always warning "Call to undefine function")
NETBEANS (Not support custom php code formatter)....

You see any IDE complete with Yii please write support with full options to support actions to improve Yii dev. Thanks